Journal of Applied Crystallography最新文献

{"title":"Mapping adsorption on ionic surfaces via a pairwise potential-based high-throughput approach.","authors":"Eric Mates-Torres, Piero Ugliengo, Albert Rimola","doi":"10.1107/S1600576725005230","DOIUrl":"10.1107/S1600576725005230","url":null,"abstract":"<p><p>Understanding molecular adsorption on ionic surfaces is crucial for a variety of chemical applications, from heterogeneous catalysis to prebiotic chemistry. Traditional approaches for identifying adsorption sites often rely on computationally expensive methods such as density functional theory (DFT), which limits their applicability to chemically complex surfaces. In this work, we propose an automated high-throughput approach to obtain a complete picture of the adsorbate-surface interaction by means of pairwise Coulomb and Lennard-Jones potentials. Using a grid-based surface scan to calculate per-site potential energies of adsorption, this method efficiently predicts global adsorption minima and all potential binding modes of a surface-adsorbate system, with the only user input being the surface CIF. Our approach is validated by studying formaldehyde (H₂CO) adsorption on forsterite (Mg₂SiO₄), a common silicate, and l-cysteine adsorption on cadmium sulfide (CdS). The predicted adsorption configurations and energies are compared with DFT values in the literature, showing good agreement and confirming the accuracy of our method. Our workflow provides a rapid means of exploring large configurational spaces and identifying stable adsorption structures, making it particularly useful for complex surfaces with multiple interaction sites. The simplicity of the model, combined with its accuracy, suggest it could be employed to discover new catalytic pathways on chemically complex ionic surfaces.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"58 Pt 4","pages":"1462-1468"},"PeriodicalIF":2.8,"publicationDate":"2025-07-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12321012/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144789137","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Machine learning assisted nanobeam X-ray diffraction based analysis on hydride vapor-phase epitaxy GaN.","authors":"Zhendong Wu, Yusuke Hayashi, Tetsuya Tohei, Kazushi Sumitani, Yasuhiko Imai, Shigeru Kimura, Akira Sakai","doi":"10.1107/S1600576725004169","DOIUrl":"10.1107/S1600576725004169","url":null,"abstract":"<p><p>Nanobeam X-ray diffraction (nanoXRD) is a powerful tool for collecting <i>in situ</i> crystal structure information with high spatial resolution and data acquisition rate. However, analyzing the enormous amount of data produced by these high-throughput experiments for defect recognition or discovering hidden structural features becomes challenging. Machine learning (ML) methods have become attractive recently due to their outstanding performance in analyzing large data sets. This research utilizes an ML algorithm, uniform manifold approximation and projection (UMAP), to enhance the nanoXRD-based crystal structure analysis of a cross-sectional hydride vapor-phase epitaxy GaN wafer. Compared with the results obtained by conventional fitting, UMAP gives a more precise categorization of crystal structure based on the raw three-dimensional ω-2θ-φ diffraction patterns. The property that UMAP embeds the high-dimensional data while retaining the data structure is valuable in guiding the analysis of nanoXRD profiles. This research also demonstrates the capability of UMAP in analyzing other spectroscopic or diffraction data sets to guide crystal structure investigations.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"58 Pt 4","pages":"1205-1219"},"PeriodicalIF":2.8,"publicationDate":"2025-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12321036/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144789136","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Kinetics of light-induced mesophase transitions in azo-benzene amphiphiles containing lyotropic liquid crystals.","authors":"Svenja C Hövelmann, Michael Röhrl, Ella Dieball, Michelle Dargasz, Jule Kuhn, Rajendra P Giri, Franziska Reise, Dmytro Soloviov, Clement E Blanchet, Michael Paulus, Thisbe K Lindhorst, Bridget M Murphy","doi":"10.1107/S1600576725004923","DOIUrl":"10.1107/S1600576725004923","url":null,"abstract":"<p><p>This study focuses on the kinetics of light-induced mesophase transitions in lyotropic liquid crystals containing a mixture of phospho-lipids and azo-benzene amphiphiles. Lipid membranes organize in a wide range of morphologies, directly influencing their functionality and the efficiency of associated components such as proteins. Transitions between mesophases occur naturally during membrane fusion and can also be triggered by multiple factors, such as pH, salinity, temperature and light. Employing light to isomerize artificial photoswitchable lipids in mixed model membranes containing 1,2-dipalmitoyl-phos-pha-tidylcholine or 1,2-didecanoyl-phosphatidylcholine revealed light-induced structural changes including mesophase transitions from a lamellar to a cubic <i>Pn</i>3<i>m</i> phase. Performing time-resolved small-angle X-ray scattering measurements, the kinetics of the change in membrane repeat distance and the transition from a lamellar to a bicontinuous cubic phase could be captured on the timescale of tens of seconds. The results demonstrate new possibilities for investigating intermediate states during mesophase transitions that are important to understand membrane fusion, and they highlight the potential of photoswitchable lipids for designing bespoke drug delivery systems.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"58 Pt 4","pages":"1322-1331"},"PeriodicalIF":2.8,"publicationDate":"2025-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12321011/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144789135","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Differentiating the solution structures and stability of transthyretin tetramer complexed with tolcapone and tafamidis using SEC-SWAXS and NMR.","authors":"Orion Shih, Yu-Chen Feng, Sashank Agrawal, Kuei-Fen Liao, Yi-Qi Yeh, Je-Wei Chang, Tsyr-Yan Yu, U-Ser Jeng","doi":"10.1107/S1600576725004716","DOIUrl":"10.1107/S1600576725004716","url":null,"abstract":"<p><p>Human transthyretin (TTR) is a homotetrameric protein involved in transporting thyroxine (T4) and retinol-binding protein within serum and cerebrospinal fluid. The disassociation of TTR's tetrameric structure can lead to the formation of biologically toxic TTR amyloid fibrils. Tolcapone, a small molecule currently under clinical trial, has shown potential as a TTR stabilizer and may act as an alternative to tafamidis, the conventional therapeutic agent used to prevent TTR dissociation. Using size-exclusion-chromatography-based small- and wide-angle X-ray scattering (SEC-SWAXS) complemented by nuclear magnetic resonance (NMR) spectroscopy, this study reveals the solution conformations of Apo-TTR and TTR complexed with tolcapone and tafamidis. Our results indicate that both compounds can bind similarly to the two T4 sites of TTR, leading to a small increase in the radius of gyration from 24.3 ± 0.1 Å (Apo-TTR) to 25.8 ± 0.1 Å. Consequently, both compounds largely stabilize the TTR against dissociation, denaturation and oligomerization up to 8 <i>M</i> urea, whereas Apo-TTR starts to denature at this concentration and forms larger oligomers at 8 <i>M</i> urea. Additionally, under a reduced TTR-drug mixing ratio of 1:1, which targets only one T4 site, tafamidis more effectively stabilizes the TTR tetrameric conformation at 8 <i>M</i> urea, a difference attributed to its higher affinity for the first T4 site. These results illustrate an effective strategy for investigating protein-drug interactions by examining the solution conformations of protein-drug complexes under physiological conditions, providing structural hints to the design of therapeutic agents targeting TTR.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"58 Pt 4","pages":"1373-1383"},"PeriodicalIF":2.8,"publicationDate":"2025-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12321038/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144789229","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Small-angle scattering studies on diverse peptide-based nanotube and helical ribbon structures reveal distinct form and structure factors.","authors":"Ian W Hamley, Valeria Castelletto","doi":"10.1107/S1600576725004637","DOIUrl":"10.1107/S1600576725004637","url":null,"abstract":"<p><p>Peptide-based nanotubes are bio-based self-assembled nanostructures with intriguing structural and functional properties. The structure of such nanotubes can be probed in detail using small-angle scattering experiments due to the typical length scales, <i>i.e.</i> diameter and wall thickness of the nanotubes, which span the range accessible in small-angle X-ray scattering (SAXS) or small-angle neutron scattering (SANS) studies. Here, we present SAXS data for several classes of peptide and lipopeptide systems previously studied by our group, as well as newly reported data for model short lysine-sequence lipopeptides. Previous data are re-examined using more accurate models for data plotted on Kratky plots, which emphasizes fine details of nanotube structure. In some cases, consideration of structure-factor effects is necessary to allow for the coexisting structures, and a lamellar structure factor is used to describe this. In other cases, such as several examples of surfactant-like peptides, only a form factor has to be considered to accurately fit the measured SAXS data. In these cases, a form factor for hollow nanotubes with a Gaussian bilayer profile to represent the layered peptide ordering in the nanotube walls is used to model the data. A general expression for the cross section scattering form factor is provided, which can be used for any scattering density profile (electron density for SAXS or scattering length density for SANS) across the wall. This is analysed along with the form factor for multishell (multiwall) nanotube structures with a series of slabs to represent the scattering density profile. For lipopeptides C₁₆-KFK and C₁₆-K (C₁₆ indicates a hexa-decyl lipid chain), SAXS data show aperiodicity in the form-factor oscillations, as well as apparent broad structure-factor peaks. These features cannot be fitted using solely nanotube form-factor models, this being ascribed to the presence of coexisting structures. Lastly, for comparison, the form factors for helical ribbon and cochleate (scroll) structures are evaluated for several examples, since in many cases electron microscopy of peptide- and lipopeptide-based nanotube systems reveals the coexistence of nanotubes with such structures, related to nanotubes.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"58 Pt 4","pages":"1311-1321"},"PeriodicalIF":2.8,"publicationDate":"2025-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12321017/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144789144","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"CIF extension for <i>Visual Studio Code</i>.","authors":"Kaisa Helttunen, Heikki Kainulainen","doi":"10.1107/S1600576725005217","DOIUrl":"10.1107/S1600576725005217","url":null,"abstract":"<p><p><i>Visual Studio Code</i> (<i>VS Code</i>) is a popular text editor and integrated development environment commonly used in software development. The crystallographic information file (CIF) language extension makes syntax highlighting, auto completion, error checking and hover information available for crystallographers reading and editing CIFs. The language extension features are available for all files following the CIF syntax, including CIF dictionary files. The design and features of the <i>VS Code</i> CIF extension are presented.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"58 Pt 4","pages":"1469-1475"},"PeriodicalIF":2.8,"publicationDate":"2025-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12321009/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144789226","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Practical neutron detection modalities for industrial use available at a time-of-flight small-angle scattering instrument.","authors":"Satoshi Koizumi, Kazuki Mita","doi":"10.1107/S1600576725004479","DOIUrl":"10.1107/S1600576725004479","url":null,"abstract":"<p><p>We report the latest advances of the iMATERIA instrument, namely, time-of-flight small-angle neutron scattering (SANS) specifically for measurements in the manufacturing and energy industries. Observations are available that are multi-scale (from a minimum <i>q</i> _min = 0.007 Å^-1 to a maximum <i>q</i> = 30 Å^-1), multi-time domain (>0.5 s) and multi-contrast by dynamical nuclear polarization. Multi-angle (or stereo) observation of film specimens can bridge between conventional SANS and reflectivity measurements. For multi-analysis, we have developed real-time simultaneous SANS and neutron radiography (NR), targeting polymer electrolyte fuel cells. In the future, we plan to establish simultaneous triple-analysis combining SANS, NR and prompt γ-ray analysis. By scanning with a beam of 1 mm² in size, such analysis enables the mapping of structural parameters determined by SANS and elemental composition determined by prompt γ-ray analysis on the image obtained by NR.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"58 Pt 4","pages":"1360-1372"},"PeriodicalIF":2.8,"publicationDate":"2025-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12321020/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144789143","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"<i>PRINSAS 2.0</i>: a Python-based graphical user interface tool for fitting polydisperse spherical pore models in small-angle scattering analysis of porous materials.","authors":"Phung Nhu Hao Vu, Andrzej P Radlinski, Tomasz Blach, John Daniels, Klaus Regenauer-Lieb","doi":"10.1107/S1600576725004315","DOIUrl":"10.1107/S1600576725004315","url":null,"abstract":"<p><p>Despite the growing use of small- and ultra-small-angle scattering (SAS/USAS) across various fields, data processing remains challenging due to the complexity of SAS analysis and the limited accessibility of existing analysis software. These issues are addressed with <i>PRINSAS 2.0</i>, a portable Python-based tool with an intuitive graphical user interface. It enables efficient fitting of the polydisperse spherical pore model to SAS data and is specifically designed for porous materials often encountered in geoscience. This paper outlines the scientific and mathematical foundations of the software, along with its numerical implementation, to provide users with theoretical context and to support future development. The software was tested and validated using data from a range of geological and engineered porous samples measured at various neutron scattering facilities, ensuring broad compatibility. Additional validation using synthetic data sets, along with comparisons with existing pore size distribution fitting tools, confirmed its robustness in recovering predefined pore size distributions. <i>PRINSAS 2.0</i> offers wide accessibility while ensuring that the fit results adhere closely to the underlying theoretical model, making it a practical tool for non-specialist users of SAS techniques. It also integrates seamlessly with larger Python-based SAS analysis frameworks, while remaining fully functional as a standalone application.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"58 Pt 4","pages":"1486-1495"},"PeriodicalIF":2.8,"publicationDate":"2025-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12321026/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144789221","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A model for out-of-phase boundary induced X-ray diffraction peak profile changes in Aurivillius oxide thin films.","authors":"Roger W Whatmore, Debismita Dutta, Lynette Keeney","doi":"10.1107/S1600576725004091","DOIUrl":"10.1107/S1600576725004091","url":null,"abstract":"<p><p>Layered crystal structures, such as the Ruddlesden-Popper and Aurivillius families of layered perovskites, have long been studied for their diverse range of functionalities. The Aurivillius family has been extensively studied for its ferroelectric properties and potential applications in various fields, including multiferroic memories. A new analytical model is presented here that explains how out-of-phase boundaries (OPBs) in epitaxial thin films of layered materials affect X-ray diffraction (XRD) peak profiles. This model predicts which diffraction peaks will split and the degree of splitting in terms of simple physical parameters that describe the nanostructure of the OPBs, specifically the structural displacement perpendicular to the layers when moving across the OPB, the angle made by the OPB at the thin-film-substrate interface, and the OPB periodicity and its statistical distribution. The model was applied to epitaxial thin films of two Aurivillius oxides, SrBi₂(Ta,Nb)O₉ (SBTN) and Bi₄Ti₃O₁₂ (BiT), and its predictions were compared with experimental XRD data for these materials. The results showed good agreement between the predicted and observed peak splitting as a function of OPB periodicity for SBTN and for an XRD profile taken from a BiT thin film containing a well characterized distribution of OPBs. These results have proven the model's validity and accuracy. The model provides a new framework for analysing and characterizing this class of defect structures in layered systems containing OPBs.</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"58 Pt 4","pages":"1191-1204"},"PeriodicalIF":2.8,"publicationDate":"2025-07-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12321024/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144789223","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Two metrics for quantifying systematic errors in diffraction experiments: systematic errors in the variance of the observed intensities and agreement factor gap.","authors":"Julian Henn","doi":"10.1107/S1600576725004376","DOIUrl":"10.1107/S1600576725004376","url":null,"abstract":"<p><p>The increase in the weighted agreement factor due to systematic errors in single-crystal X-ray and neutron diffraction experiments can be quantified precisely, provided the estimated standard uncertainties of the observed intensities, s.u.(<i>I</i> _obs), are sufficiently accurate. The increase in the weighted agreement factor quantifies the 'costs' of the systematic errors. This is achieved by comparison with the lowest possible weighted agreement factor for the specific data set. Application to 314 published data sets from inorganic, metal-organic and organic compounds shows that systematic errors increase the weighted agreement factor by a surprisingly large factor of <i>g</i> = 3.31 (or more) in 50% of the small-molecule data sets from the sample. Examples of twinning, disorder, neglect of bonding densities and low-energy contamination are taken from the literature and examined with respect to the increase in the weighted agreement factor, which is typically less than three. The large value <i>g</i> = 3.31 for the supposedly simple case of rather small molecules, as opposed to macromolecules, is interpreted as a warning sign that there are not only the expected remaining systematic errors, like not-modelled disorder, unrecognized twinning or neglect of bonding electrons or similar errors, but additionally a common systematic error of insufficiently accurate s.u.(<i>I</i> _obs). Inadequate s.u.(<i>I</i> _obs) may not just compromise the model parameters and model parameter errors; they are also a threat to the whole data quality evaluation procedure that relies crucially on adequate s.u.(<i>I</i> _obs).</p>","PeriodicalId":14950,"journal":{"name":"Journal of Applied Crystallography","volume":"58 Pt 4","pages":"1174-1184"},"PeriodicalIF":2.8,"publicationDate":"2025-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12321034/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144789236","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"材料科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}